[gmx-users] CHARMM and FEP calculations
Mark.Abraham at anu.edu.au
Mon Aug 27 00:52:04 CEST 2012
On 24/08/2012 11:28 PM, Wright, Louise wrote:
> I asked a similar question a year ago about implementing CMAP in FEP calculations for gromacs 4.5.4. At the time I could not get the simulation to run with CMAP as it came up with:
> Fatal error:
>> Function type CMAP Dih. not implemented in ip_pert
> Helpfully, Mark suggested a modification to the code to get round this issue, but I am unclear as to whether in the newer version of gromacs (4.5.5) CMAP terms can actually be scaled from state A to state B or whether for all values of lambda this part of the potential remains in state A even if I were to manually write state B CMAP terms in the topology file and the code no longer gives a warning.
I expect the latter, since
no mention of CMAP and FEP. Someone would have to want to do the coding
and testing work to make this possible.
> In addition, for CHARMM, and other FFs, there are some dihedrals which have multiple potentials, using the dihedral function type 9. I have manually specified the state B parameters for these (and all other dihedrals) in my topology file but get the error message:
> Cannot automatically perturb a torsion with multiple terms to different
> Please specify perturbed parameters manually for this torsion in your
This error pertains to what grompp can look up in ffbonded.itp for this
interaction, and is perhaps over-zealous, but without seeing the
relevant file fragments it's hard to say anything.
> Is there a way to implement scaling of these multiply defined dihedrals in FEP calculations?
> Many thanks for your help
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